Hello
I am simulating a polymeric chain in which COOH is my titrating group. I
have a -3mer system in which one of the monomers has the titrating group
attached in the form of a succinate group. I understand that two hydrogens
must be attached to each of the carboxylic oxygens to account for the ghost
proton. In my case, the protons are overlapping while doing the CpHMD and I
get a warning (vlimit exceeded along with extremely high and fluctuating
temperatures ). Is there a technique as to when to add these three extra
protons to the carboxylic oxygen. I added it after my Gaussian geometry
optimization. Should the geometry optimization be done with these 4 protons
attached to the oxygens. or Is there any other reason why vlimit can be
exceeded during the constant pH simulation. When I set my ncnstph as a very
high value say 10000, this problem does not arise.
Thank You
Rahul
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Received on Thu Oct 15 2015 - 21:00:03 PDT
